Wave Modifier Physics
This technique is not a physics based simulation, it is just a fake approximation but might yield what you are after.



Just add a single faced small planar object above your "wave surface" object.

Add a Shrink Wrap modifier to it and set it to Project mode. Make sure you tick the Negative option if necessary.



This will make your object stick to the waving surface. Now just parent whatever object your want to this plane and use Duplifaces from the Properties Window > Object Tab > Duplication > Faces to duplicate it at the face center.